7O76 | pdb_00007o76

Reversible supramolecular assembly of the anti-microbial peptide plectasin

• PDB DOI: https://doi.org/10.2210/pdb7O76/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Pseudoplectania nigrella
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2021-04-13 Released: 2022-06-29 
• Deposition Author(s): Pohl, C., Noergaard, N., Harris, P.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 
  0.178 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.143 (DCC) 

Starting Model: experimental

Literature

pH- and concentration-dependent supramolecular assembly of a fungal defensin plectasin variant into helical non-amyloid fibrils.

Pohl, C., Effantin, G., Kandiah, E., Meier, S., Zeng, G., Streicher, W., Segura, D.R., Mygind, P.H., Sandvang, D., Nielsen, L.A., Peters, G.H.J., Schoehn, G., Mueller-Dieckmann, C., Noergaard, A., Harris, P.

(2022) Nat Commun 13: 3162-3162

• PubMed: 35672293 
• DOI: https://doi.org/10.1038/s41467-022-30462-w
• Primary Citation Related Structures: 
  7O76, 7OAE, 7OAG


• PubMed Abstract: 
  

  Self-assembly and fibril formation play important roles in protein behaviour. Amyloid fibril formation is well-studied due to its role in neurodegenerative diseases and characterized by refolding of the protein into predominantly β-sheet form. However, much less is known about the assembly of proteins into other types of supramolecular structures. Using cryo-electron microscopy at a resolution of 1.97 Å, we show that a triple-mutant of the anti-microbial peptide plectasin, PPI42, assembles into helical non-amyloid fibrils. The in vitro anti-microbial activity was determined and shown to be enhanced compared to the wildtype. Plectasin contains a cysteine-stabilised α-helix-β-sheet structure, which remains intact upon fibril formation. Two protofilaments form a right-handed protein fibril. The fibril formation is reversible and follows sigmoidal kinetics with a pH- and concentration dependent equilibrium between soluble monomer and protein fibril. This high-resolution structure reveals that α/β proteins can natively assemble into fibrils.

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Organizational Affiliation: 
• Novozymes A/S, Bagsvaerd, Denmark. [e-mail].
Technical University of Denmark, Department of Chemistry, Kgs. Lyngby, Denmark. [e-mail].
Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden. [e-mail].
Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology, F-38000, Grenoble, France.
European Synchrotron Radiation Facility, Grenoble, France.
Technical University of Denmark, Department of Chemistry, Kgs. Lyngby, Denmark.
DFM A/S (Danish National Metrology Institute), Hoersholm, Denmark.
Novo Nordisk, Bagsvaerd, Denmark.
Novozymes A/S, Bagsvaerd, Denmark.
NanoTemper Technologies GmbH, Muenchen, Germany.
Ascendis Pharma A/S, Hellerup, Denmark.
Chr. Hansen A/S, Hoersholm, Denmark.
Technical University of Denmark, Department of Chemistry, Kgs. Lyngby, Denmark. [e-mail].
Department of Chemistry, University of Copenhagen, Copenhagen, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 4.52 kDa 
• Atom Count: 352 
• Modeled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fungal defensin plectasin	A [auth XXX]	40	Pseudoplectania nigrella	Mutation(s): 0  Gene Names: DEF
UniProt
Find proteins for Q53I06 (Pseudoplectania nigrella) Explore Q53I06  Go to UniProtKB:  Q53I06

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth XXX]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free:  0.178 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.143 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.678	α = 90
b = 20.093	β = 104.279
c = 32.546	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Pohl, C., Noergaard, N., Harris, P.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	675074

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary